Normal pen is subtracted before percentage pen meaning that if your opponent have 100 armor and you got 50% armor pen and 50 flat armor pen it will first substract the 50 flat. Then he will have 50 left and then after the percentage removal 25.
If you only had 50% pen he will land half of his original armor: 50.
Formel for opponents armor against your attacks: (armor-armorpen)*(1-percentagearmorpen)
Conclusion: Last Whisper lower's the effectivness of armor pen with 40%.

Really good guide. I just wonder one thing which is why do you have penetretion marks and quints when you buy last whisper? Together with masterles you already got 50% armor pen meaning that half of your normal armor pen will take effect, wouldn't ad runes be more effectiv?